NPASS Compound

Structure

NPC269030 OpenBabel06302215552D 32 35 0 0 1 0 0 0 0 0999 V2000 -0.8660 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0622 2.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 19 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 9 1 0 0 0 0 5 6 1 0 0 0 0 5 8 1 0 0 0 0 6 7 1 0 0 0 0 10 9 1 1 0 0 0 10 11 1 0 0 0 0 10 15 1 0 0 0 0 11 12 1 0 0 0 0 11 18 1 6 0 0 0 12 13 1 0 0 0 0 12 17 1 1 0 0 0 13 14 1 0 0 0 0 13 16 1 6 0 0 0 14 15 1 0 0 0 0 19 29 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 20 32 1 0 0 0 0 21 22 2 0 0 0 0 21 23 1 0 0 0 0 23 28 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 24 31 1 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 30 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	450.08
Volume:	404.641
LogP:	0.544
LogD:	-0.073
LogS:	-3.991
# Rotatable Bonds:	3
TPSA:	210.51
# H-Bond Aceptor:	12
# H-Bond Donor:	8
# Rings:	4
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.244
Synthetic Accessibility Score:	4.096
Fsp3:	0.25
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	3
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.398
MDCK Permeability:	6.957237019378226e-06
Pgp-inhibitor:	0.025
Pgp-substrate:	0.975
Human Intestinal Absorption (HIA):	0.543
20% Bioavailability (F20%):	0.085
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.009
Plasma Protein Binding (PPB):	91.01207733154297%
Volume Distribution (VD):	0.846
Pgp-substrate:	14.366711616516113%

ADMET: Metabolism

CYP1A2-inhibitor:	0.186
CYP1A2-substrate:	0.057
CYP2C19-inhibitor:	0.02
CYP2C19-substrate:	0.043
CYP2C9-inhibitor:	0.158
CYP2C9-substrate:	0.119
CYP2D6-inhibitor:	0.066
CYP2D6-substrate:	0.142
CYP3A4-inhibitor:	0.058
CYP3A4-substrate:	0.007

ADMET: Excretion

Clearance (CL):	3.129
Half-life (T1/2):	0.931

ADMET: Toxicity

hERG Blockers:	0.31
Human Hepatotoxicity (H-HT):	0.151
Drug-inuced Liver Injury (DILI):	0.982
AMES Toxicity:	0.729
Rat Oral Acute Toxicity:	0.016
Maximum Recommended Daily Dose:	0.03
Skin Sensitization:	0.942
Carcinogencity:	0.029
Eye Corrosion:	0.003
Eye Irritation:	0.801
Respiratory Toxicity:	0.037

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC269030

Natural Product ID:	NPC269030
*Common Name:**	FRXOVWDFSLBWFC-RGOKGAOMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	FRXOVWDFSLBWFC-RGOKGAOMSA-N
Standard InCHI:	InChI=1S/C20H18O12/c21-7-3-8(22)13-11(4-7)31-19(17(28)16(13)27)6-1-9(23)14(25)12(2-6)32-20-18(29)15(26)10(24)5-30-20/h1-4,10,15,18,20-26,28-29H,5H2/t10-,15+,18-,20+/m1/s1
SMILES:	c1c(cc(c(c1O)O)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O)c1c(c(=O)c2c(cc(cc2o1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	100952311
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO15432	Sarcodon aspratus	Species	Thelephoraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15665489]
NPO4485	Lamellodysidea herbacea	Species	Dysideidae	Eukaryota	n.a.	Indonesian	n.a.	PMID[17311456]
NPO14752	Sinopodophyllum emodi	Species	Berberidaceae	Eukaryota	roots and rhizomes	n.a.	n.a.	PMID[21570846]
NPO4485	Lamellodysidea herbacea	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	PMID[28841316]
NPO3860	Allium victorialis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5517	Rhododendron tomentosum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3860	Allium victorialis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3860	Allium victorialis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5517	Rhododendron tomentosum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO890	Remijia pedunculata	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15616	Solanum toxicarum	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO238	Lobelia st	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8834	Cellulomonas biazotea	Species	Cellulomonadaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO4485	Lamellodysidea herbacea	Species	Dysideidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11880	Latua pubiflora	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15240	Saracha viscosa	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12622	Rudbeckia hirta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3200	Arthrophytum leptocladum	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO13289	Frullania brittoniae	Species	Frullaniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3860	Allium victorialis	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6239	Corbicula fluminea	Species	Corbiculidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14271	Spongia australis	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11098	Stelletta inconspicua	Species	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14752	Sinopodophyllum emodi	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27957.1	Pinus densiflora var. densiflora	Varieties	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14661	Blepharis sindica	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15150	Phebalium gracile	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9283	Trichia favoginea	Species	Trichiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14035	Cladosporium tenuissimum	Species	Cladosporiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15432	Sarcodon aspratus	Species	Thelephoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14156	Fragaria indica	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC269030 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	464
0.1-0.2	1909
0.2-0.3	4390
0.3-0.4	9985
0.4-0.5	8058
0.5-0.6	4193
0.6-0.7	5204
0.7-0.8	5215
0.8-0.85	1552
0.85-0.9	1137
0.9-0.95	418
0.95-1	172

Similarity Score	Similarity Level	Natural Product ID

Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC269030 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	417
0.1-0.2	969
0.2-0.3	2074
0.3-0.4	2664
0.4-0.5	1718
0.5-0.6	866
0.6-0.7	279
0.7-0.8	126
0.8-0.85	11
0.85-0.9	17
0.9-0.95	8
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data